Hi,
Because your cuffcompare tool runs on a cluster, please ensure that
$TEMP on your Galaxy server is set to a directory which is shared
across
the cluster. By default temporary files will be created in /tmp, and
this directory is local to each system.
--nate

It turns out this problem may also arise from a mismatch between the
version of Cuffcompare that Galaxy expects and the version of
Cuffcompare actually present on the system.
Specifically, up to galaxy-central changeset 4789:d258d5bf9843, Galaxy
expects Cuffcompare version 0.9.2 or lower. If you were using
Cuffcompare version 0.9.3, you would get this error. As of galaxy-
central changeset 4780:8273a8243639, Galaxy expects and works
correctly with Cufflinks/Cuffcompare version 0.9.3
You can get this changeset by pulling directly from our in-development
repository at:
http://bitbucket.org/galaxy/galaxy-central
or by waiting for our next stable release, which should hopefully be
out later this week.
Thanks,
J.
J.